Cipro and Flagyl are first-line meds for pouchitis, but not for cuffitis or SIBO. My SIBO was treated (successfully) with a few months of doxycycline. Other doctors seem to be using Xifaxan (rifaximin). Cuffitis is often treated with mesalamine suppositories (Canasa) or enemas, or rectal steroids (e.g. proctofoam).
I’ll echo the suggestion of a bacterial probiotic. A couple of weeks of a hefty dose of Visbiome might be helpful.